The original, approved EA for the project (
http://www.toronto.ca/involved/projects/eglinton_crosstown_lrt/epr/executive-summary.pdf) covers the launch site east of Black Creek Drive since the western terminus of the original midtown tunnel was Keele. They wouldn't be able to legally commence construction without an approved EA.
The EA update will cover the new underground portions of the line. Basically, what they're doing is digging the hole for the tunnel boring machines at the location they were originally to be launched. You raise an interesting question though. When the EA is updated to permit additional tunnel west of the launch site (to Jane), how will they dig the tunnel? Will they send bores both east and west from the launch site? They may just cut and cover the segment from the Black Creek launch site to the new western terminus.
Another question is will Tim Hudak fill in the TBM launch site after the election in October?